Hi,
thanks for nice suggestions,
>> Just ensure that the ff parameters are kept as in the original paper even if you need to change the name of the atom type.
the paper I mentioned was in 2008, at that time I think p5 atom type was available, but they still used p4!
and also can you please suggest something any reason regarding "S" configuration they used.
CHARMM GUI provides R lipids. But Also I cant find standard paper reference saying lipids exist in R or S form so they should be used for simulations. Just using R or S blindly looses the importance of stereochemitry we learnt in Junior schools :-)
________________________________
From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
To: Jio M <jiomm.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Friday, July 13, 2012 2:23 PM
Subject: Re: [AMBER] lipid params
Without being a major expert ...
My feeling at the moment is that for many questions you can safely use
gaff parameters with appropriate surface tension (lipid11 should be
similar, home I am not sayoing something wrong, did not work with
lipid11 yet). Just monitor during the simulations some properties of the
membrane and make sure that you are in the range of experimental values.
If you are looking for the perfect membrane, you need to take a good
look at the literature describing the effects of surface tension in
lipid simulations or you might need to switch to CHARMM36 (which might
not be perfect either, but seems to be best lipid ff described thus far).
The names of atom types might need adaptation as with new versions of
force fields names can overlap and you might need to take care of that.
Just ensure that the ff parameters are kept as in the original paper
even if you need to change the name of the atom type.
As for the lipid11 without surface tension, I believe the best strategy
is to wait for the publications and see how well it does. Of course,
unless you have the time to do long tests and then you could ask the
developers to share with you the modifications for testing purposes (of
course its up to them whether they share at the moment or they also
prefer to wait until publication).
Best
Vlad
On 07/13/2012 10:35 AM, Jio M wrote:
> Dear All,
>
>
> {Sorry for long mail}
>
>
> As lipids are hot now these days on AMBER archive, I was trying to do some simulations on DMPC, which still I think not there in AT12 (that charmmlipid2amber.x supports conversion). So instead I tried using DMPC gaff params by Gould et al.'s J. Comput. Chem. Vol 29, page 24-37. But I have some doubts:
>
> 1) The atom type used for Phosphorous is p4 (gaff), which is actually should be p5. To recall the things, p4 type is for P attached to three atoms, while p5 is used for P with four atoms. What can be the reason?, I wonder to choose p4 as I see there is much difference in the bond, angles and torsional terms though compared to p5, vdw remains same.
>
> 2) Secondly the paper uses and validate many things with "S" configuration DMPC bilayer (the single residue is in "S" configuration, as provided in Richard's Bryce website). So can I assume these validations remain same for "R" configurations as DMPC lipid is R (I dont have reference for that though, but what CHARMM-GUI provides and other lipids are in R form only.). So is there any special reason 'S' lipid was used in such study? Anyhow I can use params for R also.
>
> 3) Few lipids are there now in lipid11 (that charmmlipid2amber.x uses). As far I was following recent archive mails AMBER will provide params which can be used without surface tension once it is published. So the params in lipid11 will change after it is published or these are same params which can be used without surface tension?
>
>
> regards,
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Fri Jul 13 2012 - 02:30:02 PDT
